Mike Jiang
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ggcyto |
| Branch: RELEASE_3_8 |
| Last Commit: e3dd40f |
| Last Changed Date: 2019-01-14 15:42:17 -0400 (Mon, 14 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:13 -0400 (Tue, 16 Apr 2019).
| Package 645/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggcyto 1.10.2 Mike Jiang
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ggcyto |
| Version: 1.10.2 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.10.2.tar.gz |
| StartedAt: 2019-04-16 00:17:02 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:21:11 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 248.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ggcyto.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggcyto.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggcyto_1.10.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ggcyto.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggcyto/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggcyto’ version ‘1.10.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ggcyto’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘scales’
All declared Imports should be used.
':::' call which should be '::': ‘flowWorkspace:::isNegated’
See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’
‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’
‘ggplot2:::as_gg_data_frame’ ‘ggplot2:::check_aesthetics’
‘ggplot2:::is.waive’ ‘ggplot2:::is_calculated_aes’
‘ggplot2:::make_labels’ ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’
‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’
‘ggplot2:::scales_list’ ‘ggplot2:::update_theme’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fs2dt: no visible binding for global variable ‘name’
add_ggcyto: no visible binding for global variable ‘name’
add_ggcyto: no visible binding for global variable ‘axis’
add_ggcyto: no visible binding for global variable ‘desc’
add_par: no visible global function definition for ‘modifyList’
as.ggplot: no visible binding for global variable ‘axis’
as.ggplot: no visible binding for global variable ‘name’
as.ggplot: no visible binding for global variable ‘density’
autoplot.GatingHierarchy : <anonymous>: no visible global function
definition for ‘gray’
autoplot.GatingSetList: no visible global function definition for
‘getS3method’
autoplot.ncdfFlowList: no visible global function definition for
‘getS3method’
density_fr_all : <anonymous>: no visible global function definition for
‘gray’
fortify.GatingSetList: no visible global function definition for
‘getS3method’
fortify.ncdfFlowList: no visible global function definition for
‘getS3method’
fortify.polygonGate : <anonymous>: no visible global function
definition for ‘dist’
fortify.polygonGate : <anonymous>: no visible global function
definition for ‘approx’
fortify_fs.GatingSetList: no visible global function definition for
‘getS3method’
getFlowFrame.GatingSetList: no visible global function definition for
‘getS3method’
getFlowFrame.ncdfFlowList: no visible global function definition for
‘getS3method’
ggcyto.GatingSetList: no visible global function definition for
‘getS3method’
ggcyto.flowSet: no visible binding for global variable ‘name’
ggcyto.flowSet: no visible binding for global variable ‘axis’
ggcyto.ncdfFlowList: no visible global function definition for
‘getS3method’
ggcyto_arrange: no visible binding for global variable ‘name’
Undefined global functions or variables:
approx axis density desc dist getS3method gray modifyList name
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "axis")
importFrom("stats", "approx", "density", "dist")
importFrom("utils", "getS3method", "modifyList")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot 38.327 26.740 16.455
plus-.ggcyto_GatingLayout 20.320 11.075 7.839
ggcyto.flowSet 15.338 5.965 8.952
ggcyto 8.863 7.276 5.806
geom_stats 7.837 6.088 3.048
geom_gate 5.982 4.812 3.879
replace_data 5.404 4.136 2.010
labs_cyto 4.930 3.933 1.835
ggcyto_flowSet_add 6.348 2.463 3.429
geom_overlay 4.523 4.154 2.215
ggcyto_par_set 4.588 2.922 1.878
marginalFilter 5.171 2.200 2.322
axis_x_inverse_trans 2.764 3.328 1.392
ggcyto.GatingSet 2.487 3.106 1.184
scale_x_flowJo_biexp 3.379 1.942 1.322
ggcyto_GatingSet_add 2.884 2.294 1.569
scale_x_flowCore_fasinh 2.480 2.526 1.447
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.8-bioc/meat/ggcyto.Rcheck/00check.log’
for details.
ggcyto.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggcyto ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ggcyto’ ... ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘%+%’ from package ‘ggplot2’ in package ‘ggcyto’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ggcyto)
ggcyto.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ggcyto)
Loading required package: ggplot2
Loading required package: flowCore
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: flowWorkspace
> library(vdiffr)
>
> test_check("ggcyto")
loading R object...
loading tree object...
Done
══ testthat results ═══════════════════════════════════════════════════════════
OK: 7 SKIPPED: 33 FAILED: 0
>
> proc.time()
user system elapsed
106.083 60.914 71.121
ggcyto.Rcheck/ggcyto-Ex.timings
| name | user | system | elapsed | |
| as.ggplot | 1.717 | 1.387 | 1.225 | |
| autoplot | 38.327 | 26.740 | 16.455 | |
| axis_x_inverse_trans | 2.764 | 3.328 | 1.392 | |
| compute_stats | 1.271 | 0.659 | 1.017 | |
| flowCore_asinht_trans | 0.009 | 0.016 | 0.004 | |
| fortify.ellipsoidGate | 0.035 | 0.058 | 0.012 | |
| fortify.filterList | 0.115 | 0.165 | 0.036 | |
| fortify.flowSet | 0.853 | 1.389 | 0.286 | |
| fortify.polygonGate | 0.038 | 0.054 | 0.012 | |
| fortify.rectangleGate | 0.042 | 0.062 | 0.013 | |
| fortify_fs | 1.079 | 0.797 | 0.766 | |
| geom_gate | 5.982 | 4.812 | 3.879 | |
| geom_hvline | 0.419 | 0.002 | 0.429 | |
| geom_overlay | 4.523 | 4.154 | 2.215 | |
| geom_stats | 7.837 | 6.088 | 3.048 | |
| getFlowFrame | 0.665 | 0.056 | 0.738 | |
| ggcyto.GatingSet | 2.487 | 3.106 | 1.184 | |
| ggcyto | 8.863 | 7.276 | 5.806 | |
| ggcyto.flowSet | 15.338 | 5.965 | 8.952 | |
| ggcyto_GatingSet_add | 2.884 | 2.294 | 1.569 | |
| ggcyto_arrange | 0.001 | 0.000 | 0.000 | |
| ggcyto_flowSet_add | 6.348 | 2.463 | 3.429 | |
| ggcyto_par_default | 0.007 | 0.000 | 0.007 | |
| ggcyto_par_set | 4.588 | 2.922 | 1.878 | |
| is.ggcyto | 0.738 | 0.198 | 0.756 | |
| is.ggcyto_flowSet | 1.223 | 0.982 | 0.793 | |
| is.ggcyto_par | 0.008 | 0.012 | 0.002 | |
| labs_cyto | 4.930 | 3.933 | 1.835 | |
| marginalFilter | 5.171 | 2.200 | 2.322 | |
| merge.quad.gates | 0.166 | 0.001 | 0.172 | |
| plus-.ggcyto_GatingLayout | 20.320 | 11.075 | 7.839 | |
| replace_data | 5.404 | 4.136 | 2.010 | |
| scale_x_flowCore_fasinh | 2.480 | 2.526 | 1.447 | |
| scale_x_flowJo_biexp | 3.379 | 1.942 | 1.322 | |
| scale_x_flowJo_fasinh | 2.229 | 1.774 | 1.412 | |
| scale_x_logicle | 2.349 | 2.553 | 1.325 | |
| stat_position | 0.646 | 0.037 | 0.685 | |